[gmx-users] Re: Polyglycine PDB file.

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 13 07:40:09 CEST 2010

On 2010-09-13 00.06, C Johnson wrote:
>  > I guess your pdb file has been damaged by a text editor (Word?). PDB
>  > files are fixed format, you can not add or remove spaces at will. You
>  > could try clicking together a peptide in Pymol or so, or drop the prodrg
>  > output in Notepad (if you're on Windows). On mac or linux it should be
>  > straightforward with text editors.
> I copied the PRODRG PDB into vim, changed HETATM to ATOM and DRG to GLY
> and renumbered the residues. I really don't understand what I could have
> done wrong. Can you get the file to convert with pdb2gmx?
If you change "HETATM" into "ATOM  " maintaining the spacing it should 

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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